Skills Guide

Align long reads with sublong

VerifiedSafe

Align long reads (PacBio, Oxford Nanopore) to a reference genome using sublong, with optional RNA-seq mode.

Sby Skills Guide Bot
Data & AIIntermediate
308/6/2026
Claude CodeCursorWindsurfCopilotCodex
#sublong#subread#long-read-alignment#bioinformatics#rna-seq

Recommended for

Claude CodeCursorCopilotWindsurfData scientistCodex

Our review

Aligns long FASTQ reads to a reference genome using Subread's sublong aligner, with optional RNA-seq mode.

Strengths

  • Handles PacBio and Oxford Nanopore long reads
  • Supports both genomic and RNA-seq alignment modes
  • Outputs BAM by default, with SAM as an explicit option
  • Simple command-line interface with thread control

Limitations

  • Requires a full one-block Subread index
  • Accepts only FASTQ or gzipped FASTQ input
  • Help flags (-h, --help) are unreliable; use -v for version
When to use it

Use when you need to map long reads against a single-block Subread reference index and produce BAM/SAM alignments.

When not to use it

Do not use for short-read alignment, multi-block indexes, or input formats other than FASTQ.

Security analysis

Safe
Quality score90/100

The skill only provides usage instructions for the sublong bioinformatics tool. The commands involve reading input files and writing output files with no destructive or exfiltrating operations. No network calls, shell piping, or dangerous flags are present.

No concerns found

Examples

Align long reads to a reference genome
Run sublong to align the file long_reads.fastq.gz against the reference index long_index, output BAM to long_reads.bam using 8 threads.
RNA-seq alignment of isoform reads
Use sublong in RNA-seq mode with -X to align isoform_reads.fastq.gz to the transcriptome index transcriptome_index, producing isoform_reads.bam.
Output SAM instead of BAM
Align long_reads.fastq.gz with sublong using index long_index and write the alignment as SAM using --SAMoutput.

name: sublong description: Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode. disable-model-invocation: true user-invocable: true

sublong

Quick Start

  • Command: sublong -i <index_name> -r <input.fastq> -o <output.bam>
  • Local executable: /home/vimalinx/miniforge3/envs/bio/bin/sublong
  • Full reference: See references/help.md

When To Use This Tool

  • Aligning long reads (e.g., PacBio, Oxford Nanopore) to a reference genome
  • Mapping reads against a full Subread index with a single block
  • Producing BAM or SAM output for downstream analysis
  • RNA-seq mode alignment via the -X flag

Common Patterns

# Align long genomic reads and write BAM output
sublong -i long_index -r long_reads.fastq.gz -o long_reads.bam -T 8

# Run in long-read RNA-seq mode
sublong -i transcriptome_index -r isoform_reads.fastq.gz -o isoform_reads.bam -X -T 8

# Emit SAM instead of BAM
sublong -i long_index -r long_reads.fastq.gz -o long_reads.sam --SAMoutput

Recommended Workflow

  1. Build a full one-block Subread index first, usually via subread-buildindex -F -B.
  2. Prepare long reads in FASTQ or gzipped FASTQ format.
  3. Decide whether you want standard genomic alignment or RNA-seq mode with -X.
  4. Run sublong with an explicit output file and thread count.
  5. Validate the BAM or SAM output before downstream quantification, QC, or variant analysis.

Guardrails

  • The index must be a full index with exactly one block; multi-block indexes are not supported
  • Input must be FASTQ or gzipped FASTQ; other formats are not accepted
  • Default output is BAM; use --SAMoutput explicitly if SAM format is required
  • -h is not a true help switch here. Local testing shows --help and --version both print usage text and then complain about the unrecognized option; -v is the real version flag.
  • -o is mandatory for sublong; unlike some other Subread tools, output is not optional.
  • -X switches on RNA-seq mode but does not replace the need for an index compatible with the same reference build you expect downstream.
Related skills

Prompt Engineering

Data & AI

Prompt engineering best practices and templates to maximize AI outputs.

claudeCursorWindsurf+1beginner
289
78
906
Admin

Data Visualization

Data & AI

Generates data visualizations and charts tailored to your data.

claudeCursorWindsurfintermediate
198
56
740
Admin

RAG Architecture Setup

Data & AI

Setup guide for RAG (Retrieval-Augmented Generation) architectures.

claudeCursorWindsurfadvanced
167
51
700
Admin